New chimeric RNAs in acute myeloid leukemia

Abstract

Background: High-throughput next generation sequencing (NGS) technologies enable the detection of biomarkers used for tumor classification, disease monitoring and cancer therapy. Whole-transcriptome analysis using RNA-seq is important, not only as a means of understanding the mechanisms responsible for complex diseases but also to efficiently identify novel genes/exons, splice isoforms, RNA editing, allele-specific mutations, differential gene expression and fusion-transcripts or chimeric RNA (chRNA). Methods: We used Crac, a tool that uses genomic locations and local coverage to classify biological events and directly infer splice and chimeric junctions within a single read. Crac’s algorithm extracts transcriptional chimeric events irrespective of annotation with a high sensitivity, and CracTools was used to aggregate, annotate and filter the chRNA reads. The selected chRNA candidates were validated by real time PCR and sequencing. In order to check the tumor specific expression of chRNA, we analyzed a publicly available dataset using a new tag search approach. Results: We present data related to acute myeloid leukemia (AML) RNA-seq analysis. We highlight novel biological cases of chRNA, in addition to previously well characterized leukemia chRNA. We have identified and validated 17 chRNAs among 3 AML patients: 10 from an AML patient with a translocation between chromosomes 15 and 17 (AML-t(15;17), 4 from patient with normal karyotype (AML-NK) 3 from a patient with chromosomal 16 inversion (AML-inv16). The new fusion transcripts can be classified into four groups according to the exon organization. Conclusions: All groups suggest complex but distinct synthesis mechanisms involving either collinear exons of different genes, non-collinear exons, or exons of different chromosomes. Finally, we check tumor-specific expression in a larger RNA-seq AML cohort and identify new AML biomarkers that could improve diagnosis and prognosis of AML.

Not Only Mutations Matter: Molecular Picture of Acute Myeloid Leukemia Emerging from Transcriptome Studies

“…By combining two or more gene loci, chRNAs also differ from conventional splicing variants. The existence of chRNAs in AML was proved by Ruffle et al in 2017 [177]. In RNA-seq data from three AML patients, 17 chRNAs were identified, including new PML-RARA transcripts with exon junctions not described earlier in t(15;17), and expression changes with time and treatment.…”

Chimeric RNA in Cancer and Stem Cell Differentiation

“…The presence of chimeric RNAs in cancer and precancer lesions supports their potential as biomarkers and therapeutic targets. Chimeric transcripts may provide means for oncogenesis in cancers with notably low mutational burden such as acute myeloid leukemia [ 57 , 58 ] or are perhaps veiled contributing factors to cancers with multiple oncogenic sources. Further, if proposed mechanisms for chimeric RNA-templated chromosomal translocation and activity as ceRNA are found to be true, controlled regulation of chimeric transcripts could play an important role in preventative cancer treatment.…”

Detailed analysis of public RNAseq data and long non-coding RNA: a proposed enhancement to mesenchymal stem cell characterisation

“…Most of published analyses highlighting new potential biomarkers of MSCs or fibroblasts have been restricted to a comparison between only few cell types and, as discussed, commonly described markers are not strictly distinctive. In order to assess the expression of Mlincs candidates in a large number of samples, we extracted specific 31nt k-mers from each of their sequences, as previously described [49]. These simplified but candidate-specific (oligonucleotide-like) probes allow a simple and fast presence/absence search to be made on large-scale cohorts and a direct quantification in raw fastq data.…”